Apr. 26th, 2016 Ontology Working Group Meeting
Planteome Ontology WG Zoom Meeting
- Date: Tuesday Apr. 26th, 2016
- Time: 8:15am PDT (GMT-7)
- Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/695257950
- attendees:
Agenda
Update on the plans for the PhenoHarmonIS Meeting in Montpellier, 9-13 May 2016
- Link to website: https://sites.google.com/a/cgxchange.org/cropontologycommunity/home
- http://tinyurl.com/hzsho6v
- About 70+ Participants are signed up:
- Link to the agenda,
- First day- Plenary sessions, tool demos
- GG will give an ontology 101 session
- Following days hands-on sessions
ICBO 2016 Call for Papers is open
- ICBO call for papers is open- http://icbo.cgrb.oregonstate.edu/ICBO_submission
http://icbo.cgrb.oregonstate.edu/ICBO_submission
Deadline is May 5th
Proposed Topics, with suggested lead:
- Planteome paper- LC
- Mappings- MAL
- Annotations project on rice, cassava and lentil, etc - AM
Formats:
- Extended Abstract- up to 2 pages
- Short Papers- up to 4 pages
- Full Papers- up to 6 pages
https://easychair.org/conferences/?conf=icbo2016
Papers will be published in a book of proceedings, not in a journal
AmiGO2 Update:
- New version of AmiGO is being tested on the dev.planteome site- http://dev.planteome.org
- You can preview the new drill down browser here: http://dev.planteome.org/amigo/dd_browse
- GO version: http://tomodachi.berkeleybop.org/amigo/landing
- Significant changes:
- Actual browser functionality
- Neighborhood tab (was ancestors and children)
- All relations will be displayed..?????
- annotations by species
Update from Biocuration 2016, April 10th-14th, 2016; Geneva, Switzerland
- MAL attended and presented a talk
PhenoPackets:
Plant Trait Ontology updates
- Recent revisions and changes to the equivalence axioms etc
- Planning to do release soon- by end of this month
More details TBA:
Other Items
Tabled from previous meetings:
OBA development- Chris Mungall
- CM: If there is time I would like to walk through the procedure we use to develop OBA.
- Part of this was covered in the tutorial on template-based ontology development, but we had to rush this part due to lack of time:
https://github.com/Planteome/protege-tutorial/tree/master/template-examples
- For OBA, the source of the ontology is primarily in TSVs, found here:
https://github.com/obophenotype/bio-attribute-ontology/tree/master/src/ontology/modules
- The design patterns are specified here:
https://github.com/obophenotype/bio-attribute-ontology/tree/master/src/ontology/patterns
- Together these are used to build the ontology with equivalence axioms, with the entire ontology hierarchy being inferred automatically, e.g:
Upcoming Meetings and Workshops
GARNet/Egenis Workshop: Integrating Large Data into Plant Science, April 21st-22nd 2016, Dartington Hall, Totnes, Devon
- Elizabeth and George are going, EA will present Planteome as part of her talk
Meeting in Montpellier, 9-13 May 2016
Link to tentative agenda/website: [1]
BioOntologies SIG of the Intelligent Systems for Molecular Biology (ISMB); July 8-12, 2016, Orlando, Florida
- Dates: July 8th and 9th, with July 9th being the “Phenotype Day”, focused on the systematic description of phenotypes.
- Short papers, up to 4 pages (will be published in JBMS)
- Poster abstracts, up to 1 page
- Flash updates, up to 1 page
7th International Conference on Biological Ontology and BioCreative 2016 Aug 1st to 4th, Corvallis, OR
- Link to program: ICBO + BioCreative Program
- Link to Easy Chair site: https://easychair.org/conferences/conference_info.cgi?a=10776589